1
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Njeri C, Pepenella S, Battapadi T, Bambara RA, Balakrishnan L. DNA Polymerase Delta Exhibits Altered Catalytic Properties on Lysine Acetylation. Genes (Basel) 2023; 14:genes14040774. [PMID: 37107532 PMCID: PMC10137900 DOI: 10.3390/genes14040774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
DNA polymerase delta is the primary polymerase that is involved in undamaged nuclear lagging strand DNA replication. Our mass-spectroscopic analysis has revealed that the human DNA polymerase δ is acetylated on subunits p125, p68, and p12. Using substrates that simulate Okazaki fragment intermediates, we studied alterations in the catalytic properties of acetylated polymerase and compared it to the unmodified form. The current data show that the acetylated form of human pol δ displays a higher polymerization activity compared to the unmodified form of the enzyme. Additionally, acetylation enhances the ability of the polymerase to resolve complex structures such as G-quadruplexes and other secondary structures that might be present on the template strand. More importantly, the ability of pol δ to displace a downstream DNA fragment is enhanced upon acetylation. Our current results suggest that acetylation has a profound effect on the activity of pol δ and supports the hypothesis that acetylation may promote higher-fidelity DNA replication.
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Affiliation(s)
- Catherine Njeri
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Sharon Pepenella
- Department of Microbiology and Immunology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Tripthi Battapadi
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Robert A Bambara
- Department of Microbiology and Immunology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
- Indiana University Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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2
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Dannenberg RL, Cardina JA, Pytko KG, Hedglin M. Tracking of progressing human DNA polymerase δ holoenzymes reveals distributions of DNA lesion bypass activities. Nucleic Acids Res 2022; 50:9893-9908. [PMID: 36107777 PMCID: PMC9508823 DOI: 10.1093/nar/gkac745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/10/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
During DNA replication, DNA lesions in lagging strand templates are initially encountered by DNA polymerase δ (pol δ) holoenzymes comprised of pol δ and the PCNA processivity sliding clamp. These encounters are thought to stall replication of an afflicted template before the lesion, activating DNA damage tolerance (DDT) pathways that replicate the lesion and adjacent DNA sequence, allowing pol δ to resume. However, qualitative studies observed that human pol δ can replicate various DNA lesions, albeit with unknown proficiencies, which raises issues regarding the role of DDT in replicating DNA lesions. To address these issues, we re-constituted human lagging strand replication to quantitatively characterize initial encounters of pol δ holoenzymes with DNA lesions. The results indicate pol δ holoenzymes support dNTP incorporation opposite and beyond multiple lesions and the extent of these activities depends on the lesion and pol δ proofreading. Furthermore, after encountering a given DNA lesion, subsequent dissociation of pol δ is distributed around the lesion and a portion does not dissociate. The distributions of these events are dependent on the lesion and pol δ proofreading. Collectively, these results reveal complexity and heterogeneity in the replication of lagging strand DNA lesions, significantly advancing our understanding of human DDT.
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Affiliation(s)
- Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph A Cardina
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kara G Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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3
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CRL4Cdt2 Ubiquitin Ligase, A Genome Caretaker Controlled by Cdt2 Binding to PCNA and DNA. Genes (Basel) 2022; 13:genes13020266. [PMID: 35205311 PMCID: PMC8871960 DOI: 10.3390/genes13020266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/22/2022] Open
Abstract
The ubiquitin ligase CRL4Cdt2 plays a vital role in preserving genomic integrity by regulating essential proteins during S phase and after DNA damage. Deregulation of CRL4Cdt2 during the cell cycle can cause DNA re-replication, which correlates with malignant transformation and tumor growth. CRL4Cdt2 regulates a broad spectrum of cell cycle substrates for ubiquitination and proteolysis, including Cdc10-dependent transcript 1 or Chromatin licensing and DNA replication factor 1 (Cdt1), histone H4K20 mono-methyltransferase (Set8) and cyclin-dependent kinase inhibitor 1 (p21), which regulate DNA replication. However, the mechanism it operates via its substrate receptor, Cdc10-dependent transcript 2 (Cdt2), is not fully understood. This review describes the essential features of the N-terminal and C-terminal parts of Cdt2 that regulate CRL4 ubiquitination activity, including the substrate recognition domain, intrinsically disordered region (IDR), phosphorylation sites, the PCNA-interacting protein-box (PIP) box motif and the DNA binding domain. Drugs targeting these specific domains of Cdt2 could have potential for the treatment of cancer.
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4
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Sobhy MA, Tehseen M, Takahashi M, Bralić A, De Biasio A, Hamdan SM. Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level. Comput Struct Biotechnol J 2021; 19:4456-4471. [PMID: 34471492 PMCID: PMC8385120 DOI: 10.1016/j.csbj.2021.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/24/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is an important component of the intricate molecular machinery for DNA replication and repair. FEN1 is a structure-specific 5' nuclease that cleaves nascent single-stranded 5' flaps during the maturation of Okazaki fragments. Here, we review our research primarily applying single-molecule fluorescence to resolve important mechanistic aspects of human FEN1 enzymatic reaction. The methodology presented in this review is aimed as a guide for tackling other biomolecular enzymatic reactions by fluorescence enhancement, quenching, and FRET and their combinations. Using these methods, we followed in real-time the structures of the substrate and product and 5' flap cleavage during catalysis. We illustrate that FEN1 actively bends the substrate to verify its features and continues to mold it to induce a protein disorder-to-order transitioning that controls active site assembly. This mechanism suppresses off-target cleavage of non-cognate substrates and promotes their dissociation with an accuracy that was underestimated from bulk assays. We determined that product release in FEN1 after the 5' flap release occurs in two steps; a brief binding to the bent nicked-product followed by longer binding to the unbent nicked-product before dissociation. Based on our cryo-electron microscopy structure of the human lagging strand replicase bound to FEN1, we propose how this two-step product release mechanism may regulate the final steps during the maturation of Okazaki fragments.
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Affiliation(s)
- Mohamed A Sobhy
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Masateru Takahashi
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Amer Bralić
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alfredo De Biasio
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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5
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Khandagale P, Thakur S, Acharya N. Identification of PCNA-interacting protein motifs in human DNA polymerase δ. Biosci Rep 2020; 40:BSR20200602. [PMID: 32314787 PMCID: PMC7189476 DOI: 10.1042/bsr20200602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/07/2020] [Accepted: 04/14/2020] [Indexed: 01/22/2023] Open
Abstract
DNA polymerase δ (Polδ) is a highly processive essential replicative DNA polymerase. In humans, the Polδ holoenzyme consists of p125, p50, p68 and p12 subunits and recently, we showed that the p12 subunit exists as a dimer. Extensive biochemical studies suggest that all the subunits of Polδ interact with the processivity factor proliferating cell nuclear antigen (PCNA) to carry out a pivotal role in genomic DNA replication. While PCNA-interacting protein motif (PIP) motifs in p68, p50 and p12 have been mapped, same in p125, the catalytic subunit of the holoenzyme, remains elusive. Therefore, in the present study by using multiple approaches we have conclusively mapped a non-canonical PIP motif from residues 999VGGLLAFA1008 in p125, which binds to the inter-domain-connecting loop (IDCL) of PCNA with high affinity. Collectively, including previous studies, we conclude that similar to Saccharomyces cerevisiae Polδ, each of the human Polδ subunits possesses motif to interact with PCNA and significantly contributes toward the processive nature of this replicative DNA polymerase.
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Affiliation(s)
- Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Shweta Thakur
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
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6
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Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A. Structure of the processive human Pol δ holoenzyme. Nat Commun 2020; 11:1109. [PMID: 32111820 PMCID: PMC7048817 DOI: 10.1038/s41467-020-14898-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/07/2020] [Indexed: 01/01/2023] Open
Abstract
In eukaryotes, DNA polymerase δ (Pol δ) bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki fragments for their ligation. We present the high-resolution cryo-EM structure of the human processive Pol δ–DNA–PCNA complex in the absence and presence of FEN1. Pol δ is anchored to one of the three PCNA monomers through the C-terminal domain of the catalytic subunit. The catalytic core sits on top of PCNA in an open configuration while the regulatory subunits project laterally. This arrangement allows PCNA to thread and stabilize the DNA exiting the catalytic cleft and recruit FEN1 to one unoccupied monomer in a toolbelt fashion. Alternative holoenzyme conformations reveal important functional interactions that maintain PCNA orientation during synthesis. This work sheds light on the structural basis of Pol δ’s activity in replicating the human genome. Pol δ bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand in eukaryotes and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki fragments for their ligation. Here, the authors present a Cryo-EM structure of the human 4-subunit Pol δ bound to DNA and PCNA in a replicating state with an incoming nucleotide in the active site.
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Affiliation(s)
- Claudia Lancey
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Muhammad Tehseen
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Vlad-Stefan Raducanu
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Fahad Rashid
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Nekane Merino
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160, Derio, Spain
| | - Timothy J Ragan
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Christos G Savva
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Manal S Zaher
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Afnan Shirbini
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Francisco J Blanco
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Samir M Hamdan
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - Alfredo De Biasio
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK.
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7
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De March M, Barrera-Vilarmau S, Crespan E, Mentegari E, Merino N, Gonzalez-Magaña A, Romano-Moreno M, Maga G, Crehuet R, Onesti S, Blanco FJ, De Biasio A. p15PAF binding to PCNA modulates the DNA sliding surface. Nucleic Acids Res 2019; 46:9816-9828. [PMID: 30102405 PMCID: PMC6182140 DOI: 10.1093/nar/gky723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/31/2018] [Indexed: 12/15/2022] Open
Abstract
p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the sliding surface. Here, we probed the atomic-scale structure of p15PAF–PCNA–DNA ternary complexes. Crystallography and MD simulations show that, when p15PAF occupies two subunits of the PCNA homotrimer, DNA within the ring channel binds the unoccupied subunit. The structure of PCNA-bound p15PAF in the absence and presence of DNA is invariant, and solution NMR confirms that DNA does not displace p15PAF from the ring wall. Thus, p15PAF reduces the available sliding surfaces of PCNA, and may function as a belt that fastens the DNA to the clamp during synthesis by the replicative polymerase (pol δ). This constraint, however, may need to be released for efficient DNA lesion bypass by the translesion synthesis polymerase (pol η). Accordingly, our biochemical data show that p15PAF impairs primer synthesis by pol η–PCNA holoenzyme against both damaged and normal DNA templates. In light of our findings, we discuss the possible mechanistic roles of p15PAF in DNA replication and suppression of DNA lesion bypass.
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Affiliation(s)
- Matteo De March
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
| | - Susana Barrera-Vilarmau
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Emmanuele Crespan
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Elisa Mentegari
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Nekane Merino
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | | | | | - Giovanni Maga
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Ramon Crehuet
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
| | - Francisco J Blanco
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Alfredo De Biasio
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy.,Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
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8
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Khandagale P, Peroumal D, Manohar K, Acharya N. Human DNA polymerase delta is a pentameric holoenzyme with a dimeric p12 subunit. Life Sci Alliance 2019; 2:2/2/e201900323. [PMID: 30885984 PMCID: PMC6424025 DOI: 10.26508/lsa.201900323] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 01/07/2023] Open
Abstract
The subunit p12 of human DNA polymerase delta (hPolδ) can dimerize, facilitating its interaction with PCNA and suggesting that hPolδ exists in a pentameric form in the cell. Human DNA polymerase delta (Polδ), a holoenzyme consisting of p125, p50, p68, and p12 subunits, plays an essential role in DNA replication, repair, and recombination. Herein, using multiple physicochemical and cellular approaches, we found that the p12 protein forms a dimer in solution. In vitro reconstitution and pull down of cellular Polδ by tagged p12 substantiate the pentameric nature of this critical holoenzyme. Furthermore, a consensus proliferating nuclear antigen (PCNA) interaction protein motif at the extreme carboxyl-terminal tail and a homodimerization domain at the amino terminus of the p12 subunit were identified. Mutational analyses of these motifs in p12 suggest that dimerization facilitates p12 binding to the interdomain connecting loop of PCNA. In addition, we observed that oligomerization of the smallest subunit of Polδ is evolutionarily conserved as Cdm1 of Schizosaccharomyces pombe also dimerizes. Thus, we suggest that human Polδ is a pentameric complex with a dimeric p12 subunit, and discuss implications of p12 dimerization in enzyme architecture and PCNA interaction during DNA replication.
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Affiliation(s)
- Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Doureradjou Peroumal
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
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9
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Gonzalez-Magaña A, Ibáñez de Opakua A, Romano-Moreno M, Murciano-Calles J, Merino N, Luque I, Rojas AL, Onesti S, Blanco FJ, De Biasio A. The p12 subunit of human polymerase δ uses an atypical PIP box for molecular recognition of proliferating cell nuclear antigen (PCNA). J Biol Chem 2019; 294:3947-3956. [PMID: 30655288 DOI: 10.1074/jbc.ra118.006391] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/11/2019] [Indexed: 12/28/2022] Open
Abstract
Human DNA polymerase δ is essential for DNA replication and acts in conjunction with the processivity factor proliferating cell nuclear antigen (PCNA). In addition to its catalytic subunit (p125), pol δ comprises three regulatory subunits (p50, p68, and p12). PCNA interacts with all of these subunits, but only the interaction with p68 has been structurally characterized. Here, we report solution NMR-, isothermal calorimetry-, and X-ray crystallography-based analyses of the p12-PCNA interaction, which takes part in the modulation of the rate and fidelity of DNA synthesis by pol δ. We show that p12 binds with micromolar affinity to the classical PIP-binding pocket of PCNA via a highly atypical PIP box located at the p12 N terminus. Unlike the canonical PIP box of p68, the PIP box of p12 lacks the conserved glutamine; binds through a 2-fork plug made of an isoleucine and a tyrosine residue at +3 and +8 positions, respectively; and is stabilized by an aspartate at +6 position, which creates a network of intramolecular hydrogen bonds. These findings add to growing evidence that PCNA can bind a diverse range of protein sequences that may be broadly grouped as PIP-like motifs as has been previously suggested.
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Affiliation(s)
- Amaia Gonzalez-Magaña
- From the CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | | | - Miguel Romano-Moreno
- From the CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | - Javier Murciano-Calles
- the Department of Physical Chemistry and Institute of Biotechnology, Universidad de Granada, Granada 18071, Spain
| | - Nekane Merino
- From the CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | - Irene Luque
- the Department of Physical Chemistry and Institute of Biotechnology, Universidad de Granada, Granada 18071, Spain
| | - Adriana L Rojas
- From the CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | - Silvia Onesti
- the Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
| | - Francisco J Blanco
- From the CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain, .,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain, and
| | - Alfredo De Biasio
- the Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy, .,the Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7HB, United Kingdom
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10
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Weßbecher IM, Brieger A. Phosphorylation meets DNA mismatch repair. DNA Repair (Amst) 2018; 72:107-114. [PMID: 30249411 DOI: 10.1016/j.dnarep.2018.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022]
Abstract
DNA mismatch repair (MMR) is a highly conserved process and ensures the removal of mispaired DNA bases and insertion-deletion loops right after replication. For this, a MutSα or MutSβ protein complex recognizes the DNA damage, MutLα nicks the erroneous strand, exonuclease 1 removes the wrong nucleotides, DNA polymerase δ refills the gap and DNA ligase I joins the fragments to seal the nicks and complete the repair process. The failure to accomplish these functions is associated with higher mutation rates and may lead to cancer, which highlights the importance of MMR by the maintenance of genomic stability. The post-replicative MMR implies that involved proteins are regulated at several levels, including posttranslational modifications (PTMs). Phosphorylation is one of the most common and major PTMs. Suitable with its regulatory force phosphorylation was shown to influence MMR factors thereby adjusting eukaryotic MMR activity. In this review, we summarized the current knowledge of the role of phosphorylation of MMR process involved proteins and their functional relevance.
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Affiliation(s)
| | - Angela Brieger
- Medical Clinic I, Biomedical Research Laboratory, Goethe-University, Frankfurt a.M., Germany.
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11
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Maneuvers on PCNA Rings during DNA Replication and Repair. Genes (Basel) 2018; 9:genes9080416. [PMID: 30126151 PMCID: PMC6116012 DOI: 10.3390/genes9080416] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/20/2022] Open
Abstract
DNA replication and repair are essential cellular processes that ensure genome duplication and safeguard the genome from deleterious mutations. Both processes utilize an abundance of enzymatic functions that need to be tightly regulated to ensure dynamic exchange of DNA replication and repair factors. Proliferating cell nuclear antigen (PCNA) is the major coordinator of faithful and processive replication and DNA repair at replication forks. Post-translational modifications of PCNA, ubiquitination and acetylation in particular, regulate the dynamics of PCNA-protein interactions. Proliferating cell nuclear antigen (PCNA) monoubiquitination elicits ‘polymerase switching’, whereby stalled replicative polymerase is replaced with a specialized polymerase, while PCNA acetylation may reduce the processivity of replicative polymerases to promote homologous recombination-dependent repair. While regulatory functions of PCNA ubiquitination and acetylation have been well established, the regulation of PCNA-binding proteins remains underexplored. Considering the vast number of PCNA-binding proteins, many of which have similar PCNA binding affinities, the question arises as to the regulation of the strength and sequence of their binding to PCNA. Here I provide an overview of post-translational modifications on both PCNA and PCNA-interacting proteins and discuss their relevance for the regulation of the dynamic processes of DNA replication and repair.
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12
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Lee MYWT, Wang X, Zhang S, Zhang Z, Lee EYC. Regulation and Modulation of Human DNA Polymerase δ Activity and Function. Genes (Basel) 2017; 8:genes8070190. [PMID: 28737709 PMCID: PMC5541323 DOI: 10.3390/genes8070190] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 12/28/2022] Open
Abstract
This review focuses on the regulation and modulation of human DNA polymerase δ (Pol δ). The emphasis is on the mechanisms that regulate the activity and properties of Pol δ in DNA repair and replication. The areas covered are the degradation of the p12 subunit of Pol δ, which converts it from a heterotetramer (Pol δ4) to a heterotrimer (Pol δ3), in response to DNA damage and also during the cell cycle. The biochemical mechanisms that lead to degradation of p12 are reviewed, as well as the properties of Pol δ4 and Pol δ3 that provide insights into their functions in DNA replication and repair. The second focus of the review involves the functions of two Pol δ binding proteins, polymerase delta interaction protein 46 (PDIP46) and polymerase delta interaction protein 38 (PDIP38), both of which are multi-functional proteins. PDIP46 is a novel activator of Pol δ4, and the impact of this function is discussed in relation to its potential roles in DNA replication. Several new models for the roles of Pol δ3 and Pol δ4 in leading and lagging strand DNA synthesis that integrate a role for PDIP46 are presented. PDIP38 has multiple cellular localizations including the mitochondria, the spliceosomes and the nucleus. It has been implicated in a number of cellular functions, including the regulation of specialized DNA polymerases, mitosis, the DNA damage response, mouse double minute 2 homolog (Mdm2) alternative splicing and the regulation of the NADPH oxidase 4 (Nox4).
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Affiliation(s)
- Marietta Y W T Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Xiaoxiao Wang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Sufang Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Zhongtao Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Ernest Y C Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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Barnes R, Eckert K. Maintenance of Genome Integrity: How Mammalian Cells Orchestrate Genome Duplication by Coordinating Replicative and Specialized DNA Polymerases. Genes (Basel) 2017; 8:genes8010019. [PMID: 28067843 PMCID: PMC5295014 DOI: 10.3390/genes8010019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/19/2016] [Accepted: 12/27/2016] [Indexed: 12/30/2022] Open
Abstract
Precise duplication of the human genome is challenging due to both its size and sequence complexity. DNA polymerase errors made during replication, repair or recombination are central to creating mutations that drive cancer and aging. Here, we address the regulation of human DNA polymerases, specifically how human cells orchestrate DNA polymerases in the face of stress to complete replication and maintain genome stability. DNA polymerases of the B-family are uniquely adept at accurate genome replication, but there are numerous situations in which one or more additional DNA polymerases are required to complete genome replication. Polymerases of the Y-family have been extensively studied in the bypass of DNA lesions; however, recent research has revealed that these polymerases play important roles in normal human physiology. Replication stress is widely cited as contributing to genome instability, and is caused by conditions leading to slowed or stalled DNA replication. Common Fragile Sites epitomize “difficult to replicate” genome regions that are particularly vulnerable to replication stress, and are associated with DNA breakage and structural variation. In this review, we summarize the roles of both the replicative and Y-family polymerases in human cells, and focus on how these activities are regulated during normal and perturbed genome replication.
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Affiliation(s)
- Ryan Barnes
- Biomedical Sciences Graduate Program, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Kristin Eckert
- Departments of Pathology and Biochemistry & Molecular Biology, The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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14
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Roles of human POLD1 and POLD3 in genome stability. Sci Rep 2016; 6:38873. [PMID: 27974823 PMCID: PMC5156928 DOI: 10.1038/srep38873] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/16/2016] [Indexed: 12/11/2022] Open
Abstract
DNA replication is essential for cellular proliferation. If improperly controlled it can constitute a major source of genome instability, frequently associated with cancer and aging. POLD1 is the catalytic subunit and POLD3 is an accessory subunit of the replicative Pol δ polymerase, which also functions in DNA repair, as well as the translesion synthesis polymerase Pol ζ, whose catalytic subunit is REV3L. In cells depleted of POLD1 or POLD3 we found a differential but general increase in genome instability as manifested by DNA breaks, S-phase progression impairment and chromosome abnormalities. Importantly, we showed that both proteins are needed to maintain the proper amount of active replication origins and that POLD3-depletion causes anaphase bridges accumulation. In addition, POLD3-associated DNA damage showed to be dependent on RNA-DNA hybrids pointing toward an additional and specific role of this subunit in genome stability. Interestingly, a similar increase in RNA-DNA hybrids-dependent genome instability was observed in REV3L-depleted cells. Our findings demonstrate a key role of POLD1 and POLD3 in genome stability and S-phase progression revealing RNA-DNA hybrids-dependent effects for POLD3 that might be partly due to its Pol ζ interaction.
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Nicolas E, Golemis EA, Arora S. POLD1: Central mediator of DNA replication and repair, and implication in cancer and other pathologies. Gene 2016; 590:128-41. [PMID: 27320729 PMCID: PMC4969162 DOI: 10.1016/j.gene.2016.06.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 02/06/2023]
Abstract
The evolutionarily conserved human polymerase delta (POLD1) gene encodes the large p125 subunit which provides the essential catalytic activities of polymerase δ (Polδ), mediated by 5′–3′ DNA polymerase and 3′–5′ exonuclease moieties. POLD1 associates with three smaller subunits (POLD2, POLD3, POLD4), which together with Replication Factor C and Proliferating Nuclear Cell Antigen constitute the polymerase holoenzyme. Polδ function is essential for replication, with a primary role as the replicase for the lagging strand. Polδ also has an important proofreading ability conferred by the exonuclease activity, which is critical for ensuring replicative fidelity, but also serves to repair DNA lesions arising as a result of exposure to mutagens. Polδ has been shown to be important for multiple forms of DNA repair, including nucleotide excision repair, double strand break repair, base excision repair, and mismatch repair. A growing number of studies in the past decade have linked germline and sporadic mutations in POLD1 and the other subunits of Polδ with human pathologies. Mutations in Polδ in mice and humans lead to genomic instability, mutator phenotype and tumorigenesis. The advent of genome sequencing techniques has identified damaging mutations in the proofreading domain of POLD1 as the underlying cause of some inherited cancers, and suggested that mutations in POLD1 may influence therapeutic management. In addition, mutations in POLD1 have been identified in the developmental disorders of mandibular hypoplasia, deafness, progeroid features and lipodystrophy and atypical Werner syndrome, while changes in expression or activity of POLD1 have been linked to senescence and aging. Intriguingly, some recent evidence suggests that POLD1 function may also be altered in diabetes. We provide an overview of critical Polδ activities in the context of these pathologic conditions.
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Affiliation(s)
- Emmanuelle Nicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sanjeevani Arora
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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Deshmukh AL, Kumar C, Singh DK, Maurya P, Banerjee D. Dynamics of replication proteins during lagging strand synthesis: A crossroads for genomic instability and cancer. DNA Repair (Amst) 2016; 42:72-81. [DOI: 10.1016/j.dnarep.2016.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 01/18/2023]
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Abstract
Base excision repair (BER) is an essential DNA repair pathway involved in the maintenance of genome stability and thus in the prevention of human diseases, such as premature aging, neurodegenerative diseases, and cancer. Protein posttranslational modifications (PTMs), including acetylation, methylation, phosphorylation, SUMOylation, and ubiquitylation, have emerged as important contributors in controlling cellular BER protein levels, enzymatic activities, protein-protein interactions, and protein cellular localization. These PTMs therefore play key roles in regulating the BER pathway and are consequently crucial for coordinating an efficient cellular DNA damage response. In this review, we summarize the presently available data on characterized PTMs of key BER proteins, the functional consequences of these modifications at the protein level, and also the impact on BER in vitro and in vivo.
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18
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Stability of the human polymerase δ holoenzyme and its implications in lagging strand DNA synthesis. Proc Natl Acad Sci U S A 2016; 113:E1777-86. [PMID: 26976599 DOI: 10.1073/pnas.1523653113] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In eukaryotes, DNA polymerase δ (pol δ) is responsible for replicating the lagging strand template and anchors to the proliferating cell nuclear antigen (PCNA) sliding clamp to form a holoenzyme. The stability of this complex is integral to every aspect of lagging strand replication. Most of our understanding comes from Saccharomyces cerevisae where the extreme stability of the pol δ holoenzyme ensures that every nucleobase within an Okazaki fragment is faithfully duplicated before dissociation but also necessitates an active displacement mechanism for polymerase recycling and exchange. However, the stability of the human pol δ holoenzyme is unknown. We designed unique kinetic assays to analyze the processivity and stability of the pol δ holoenzyme. Surprisingly, the results indicate that human pol δ maintains a loose association with PCNA while replicating DNA. Such behavior has profound implications on Okazaki fragment synthesis in humans as it limits the processivity of pol δ on undamaged DNA and promotes the rapid dissociation of pol δ from PCNA on stalling at a DNA lesion.
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Smith SJ, Hickey RJ, Malkas LH. Validating the disruption of proliferating cell nuclear antigen interactions in the development of targeted cancer therapeutics. Cancer Biol Ther 2016; 17:310-9. [PMID: 26889573 DOI: 10.1080/15384047.2016.1139247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human DNA replication and repair is a highly coordinated process involving the specifically timed actions of numerous proteins and enzymes. Many of these proteins require interaction with proliferating cell nuclear antigen (PCNA) for activation within the process. The interdomain connector loop (IDCL) of PCNA provides a docking site for many of those proteins, suggesting that this region is critically important in the regulation of cellular function. Previous work in this laboratory has demonstrated that a peptide mimicking a specific region of the IDCL (caPeptide) has the ability to disrupt key protein-protein interactions between PCNA and its binding partners, thereby inhibiting DNA replication within the cells. In this study, we confirm the ability of the caPeptide to disrupt DNA replication function using both intact cell and in vitro DNA replication assays. Further, we were able to demonstrate that treatment with caPeptide results in a decrease of polymerase δ activity that correlates with the observed decrease in DNA replication. We have also successfully developed a surface plasmon resonance (SPR) assay to validate the disruption of the PCNA-pol δ interaction with caPeptide.
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Affiliation(s)
- Shanna J Smith
- a Beckman Research Institute at City of Hope , Department of Molecular and Cellular Biology , Duarte , CA , USA
| | - Robert J Hickey
- b Beckman Research Institute at City of Hope , Department of Molecular Pharmacology , Duarte , CA , USA
| | - Linda H Malkas
- a Beckman Research Institute at City of Hope , Department of Molecular and Cellular Biology , Duarte , CA , USA
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20
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You C, Yang Y, Zhang L, Chen H, Chen Y, Chen K, Zhou Y. Comparative proteomics analysis of global cellular stress responses to hydroxyurea-induced DNA damage in HeLa cells. Cytotechnology 2014; 68:809-20. [PMID: 25519465 DOI: 10.1007/s10616-014-9832-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 11/29/2014] [Indexed: 10/24/2022] Open
Abstract
Both environmental agents and spontaneous cellular events cause serious DNA damage, threatening the integrity of the genome. In response to replication stress or genotoxic agents triggered DNA damage, degradation of p12 subunit of DNA polymerase delta (Pol δ) results in an inter-conversion between heterotetramer (Pol δ4) and heterotrimer (Pol δ3) forms and plays a significant role in DNA damage response in eukaryotic cells. In this work, we used mass spectrometry-based proteomic approach to identify those cellular stress response protein changes corresponding to the degradation of p12 in DNA-damaged HeLa cells by the treatment with hydroxyurea (HU). A total of 736 ± 13 proteins in non-treated control group and 741 ± 19 protein spots in HU-treated cells were detected, of which 34 proteins (17 up-regulated and 17 down-regulated) exhibited significantly altered protein expression levels. Their physiological roles are mainly associated with cellular components, molecular functions, and biological processes by gene ontology analysis, among which 21 proteins were mapped to KEGG pathways. They are involved in 5 primary pathways with the subsets involving 16 secondary pathways by further KEGG analysis. More interestingly, the up-regulation of translationally controlled tumor protein was further identified to be associated with p12 degradation by Western blot analysis. Our works may enlarge and broaden our view for deeply understanding how global cellular stress responds to DNA damage, which could contribute to the etiology of human cancer or other diseases that can result from loss of genomic stability.
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Affiliation(s)
- Chao You
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, China
| | - Yanhua Yang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, China
| | - Lei Zhang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, China
| | - Huiqing Chen
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, China
| | - Yan Chen
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, China
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, China
| | - Yajing Zhou
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, China.
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21
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Jarrett SG, Horrell EMW, Christian PA, Vanover JC, Boulanger MC, Zou Y, D'Orazio JA. RETRACTED: PKA-mediated phosphorylation of ATR promotes recruitment of XPA to UV-induced DNA damage. Mol Cell 2014; 54:999-1011. [PMID: 24950377 PMCID: PMC4076709 DOI: 10.1016/j.molcel.2014.05.030] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 03/28/2014] [Accepted: 05/17/2014] [Indexed: 12/21/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the authors. An investigation by the University of Kentucky (UK) recently determined that it contains fabricated and/or falsified data committed by the lead author on the paper. The results of the investigation can be viewed at https://ori.hhs.gov/content/case-summary-jarrett-stuart-g. UK identified that there were duplications and flips of panels in three figures (Figures 7D, 7E, and S3C), and original data could not be retrieved. In Figures 7D and 7E, there are inappropriate loading controls: reuse and relabeling between Figure 7D (no UV) and Figure 7E (+ UV). In Figure S3C, the loading controls for 6-4 PP (second row down) are the same as those for XPA (fourth row down), but are flipped. In both cases, the authors could not recover the original data, since primary data were stored only on a computer associated with a Storm PhosphorImager and were lost when that computer crashed. Thus, this is considered data fabrication, and the authors are retracting the paper. The authors apologize to the scientific community for any inconveniences or challenges resulting from the publication and retraction of this manuscript. Authors Stuart Jarrett and Jillian Vanover could not be reached. The remaining authors agree to the retraction.
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Affiliation(s)
- Stuart G Jarrett
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Erin M Wolf Horrell
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA; Department of Physiology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Perry A Christian
- Graduate Center for Toxicology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Jillian C Vanover
- Department of Pharmacology and Nutrition Sciences, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Mary C Boulanger
- Department of Dietetics and Human Nutrition, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Yue Zou
- Department of Biochemistry and Molecular Biology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - John A D'Orazio
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA; Department of Physiology, University of Kentucky College of Medicine, Lexington, KY 40536, USA; Graduate Center for Toxicology, University of Kentucky College of Medicine, Lexington, KY 40536, USA; Department of Pharmacology and Nutrition Sciences, University of Kentucky College of Medicine, Lexington, KY 40536, USA; Department of Dietetics and Human Nutrition, University of Kentucky College of Medicine, Lexington, KY 40536, USA; Department of Pediatrics, University of Kentucky College of Medicine, Lexington, KY 40536, USA.
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22
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Fan X, Zhang Q, You C, Qian Y, Gao J, Liu P, Chen H, Song H, Chen Y, Chen K, Zhou Y. Proteolysis of the human DNA polymerase delta smallest subunit p12 by μ-calpain in calcium-triggered apoptotic HeLa cells. PLoS One 2014; 9:e93642. [PMID: 24691096 PMCID: PMC3972206 DOI: 10.1371/journal.pone.0093642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/04/2014] [Indexed: 11/19/2022] Open
Abstract
Degradation of p12 subunit of human DNA polymerase delta (Pol δ) that results in an interconversion between Pol δ4 and Pol δ3 forms plays a significant role in response to replication stress or genotoxic agents triggered DNA damage. Also, the p12 is readily degraded by human calpain in vitro. However, little has been done for the investigation of its degree of participation in any of the more common apoptosis. Here, we first report that the p12 subunit is a substrate of μ-calpain. In calcium-triggered apoptotic HeLa cells, the p12 is degraded at 12 hours post-induction (hpi), restored thereafter by 24 hpi, and then depleted again after 36 hpi in a time-dependent manner while the other three subunits are not affected. It suggests a dual function of Pol δ by its interconversion between Pol δ4 and Pol δ3 that is involved in a novel unknown apoptosis mechanism. The proteolysis of p12 could be efficiently blocked by both calpain inhibitor ALLN and proteasome inhibitor MG132. In vitro pull down and co-immunoprecipitation assays show that the μ-calpain binds to p12 through the interaction of μ-calpain with Pol δ other three subunits, not p12 itself, and PCNA, implying that the proteolysis of p12 by μ-calpain might be through a Pol δ4/PCNA complex. The p12 cleavage sites by μ-calpain are further determined as the location within a 16-amino acids peptide 28-43 by in vitro cleavage assays. Thus, the p12/Pol δ is a target as a nuclear substrate of μ-calpain in a calcium-triggered apoptosis and appears to be a potential marker in the study of the chemotherapy of cancer therapies.
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Affiliation(s)
- Xiaoting Fan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Qian Zhang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Chao You
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Yuanxia Qian
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Jing Gao
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Peng Liu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Huiqing Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Huifang Song
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Yan Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Yajing Zhou
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
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24
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Abstract
Cellular DNA replication requires efficient copying of the double-stranded chromosomal DNA. The leading strand is elongated continuously in the direction of fork opening, whereas the lagging strand is made discontinuously in the opposite direction. The lagging strand needs to be processed to form a functional DNA segment. Genetic analyses and reconstitution experiments identified proteins and multiple pathways responsible for maturation of the lagging strand. In both prokaryotes and eukaryotes the lagging-strand fragments are initiated by RNA primers, which are removed by a joining mechanism involving strand displacement of the primer into a flap, flap removal, and then ligation. Although the prokaryotic fragments are ~1200 nucleotides long, the eukaryotic fragments are much shorter, with lengths determined by nucleosome periodicity. The prokaryotic joining mechanism is simple and efficient. The eukaryotic maturation mechanism involves many enzymes, possibly three pathways, and regulation that can shift from high efficiency to high fidelity.
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25
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Prindle MJ, Loeb LA. DNA polymerase delta in DNA replication and genome maintenance. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:666-82. [PMID: 23065663 PMCID: PMC3694620 DOI: 10.1002/em.21745] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/09/2012] [Accepted: 09/12/2012] [Indexed: 05/12/2023]
Abstract
The eukaryotic genome is in a constant state of modification and repair. Faithful transmission of the genomic information from parent to daughter cells depends upon an extensive system of surveillance, signaling, and DNA repair, as well as accurate synthesis of DNA during replication. Often, replicative synthesis occurs over regions of DNA that have not yet been repaired, presenting further challenges to genomic stability. DNA polymerase δ (pol δ) occupies a central role in all of these processes: catalyzing the accurate replication of a majority of the genome, participating in several DNA repair synthetic pathways, and contributing structurally to the accurate bypass of problematic lesions during translesion synthesis. The concerted actions of pol δ on the lagging strand, pol ϵ on the leading strand, associated replicative factors, and the mismatch repair (MMR) proteins results in a mutation rate of less than one misincorporation per genome per replication cycle. This low mutation rate provides a high level of protection against genetic defects during development and may prevent the initiation of malignancies in somatic cells. This review explores the role of pol δ in replication fidelity and genome maintenance.
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Affiliation(s)
- Marc J Prindle
- Department of Pathology, The Joseph Gottstien Memorial Cancer Research Laboratory, University of Washington, Seattle, WA 98195-7705, USA
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26
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Menezes MR, Sweasy JB. Mouse models of DNA polymerases. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:645-665. [PMID: 23001998 DOI: 10.1002/em.21731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 06/01/2023]
Abstract
In 1956, Arthur Kornberg discovered the mechanism of the biological synthesis of DNA and was awarded the Nobel Prize in Physiology or Medicine in 1959 for this contribution, which included the isolation and characterization of Escherichia coli DNA polymerase I. Now there are 15 known DNA polymerases in mammalian cells that belong to four different families. These DNA polymerases function in many different cellular processes including DNA replication, DNA repair, and damage tolerance. Several biochemical and cell biological studies have provoked a further investigation of DNA polymerase function using mouse models in which polymerase genes have been altered using gene-targeting techniques. The phenotypes of mice harboring mutant alleles reveal the prominent role of DNA polymerases in embryogenesis, prevention of premature aging, and cancer suppression.
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Affiliation(s)
- Miriam R Menezes
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
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Lee MYWT, Zhang S, Lin SHS, Chea J, Wang X, LeRoy C, Wong A, Zhang Z, Lee EYC. Regulation of human DNA polymerase delta in the cellular responses to DNA damage. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:683-698. [PMID: 23047826 DOI: 10.1002/em.21743] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 06/01/2023]
Abstract
The p12 subunit of polymerase delta (Pol δ) is degraded in response to DNA damage induced by UV, alkylating agents, oxidative, and replication stresses. This leads to the conversion of the Pol δ4 holoenzyme to the heterotrimer, Pol δ3. We review studies that establish that Pol δ3 formation is an event that could have a major impact on cellular processes in genomic surveillance, DNA replication, and DNA repair. p12 degradation is dependent on the apical ataxia telangiectasia and Rad3 related (ATR) kinase and is mediated by the ubiquitin-proteasome system. Pol δ3 exhibits properties of an "antimutator" polymerase, suggesting that it could contribute to an increased surveillance against mutagenesis, for example, when Pol δ carries out bypass synthesis past small base lesions that engage in spurious base pairing. Chromatin immunoprecipitation analysis and examination of the spatiotemporal recruitment of Pol δ to sites of DNA damage show that Pol δ3 is the primary form of Pol δ associated with cyclobutane pyrimidine dimer lesions and therefore should be considered as the operative form of Pol δ engaged in DNA repair. We propose a model for the switching of Pol δ with translesion polymerases, incorporating the salient features of the recently determined structure of monoubiquitinated proliferating cell nuclear antigen and emphasizing the role of Pol δ3. Because of the critical role of Pol δ activity in DNA replication and repair, the formation of Pol δ3 in response to DNA damage opens the prospect that pleiotropic effects may ensue. This opens the horizons for future exploration of how this novel response to DNA damage contributes to genomic stability.
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Affiliation(s)
- Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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28
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Zhou Y, Meng X, Zhang S, Lee EYC, Lee MYWT. Characterization of human DNA polymerase delta and its subassemblies reconstituted by expression in the MultiBac system. PLoS One 2012; 7:e39156. [PMID: 22723953 PMCID: PMC3377666 DOI: 10.1371/journal.pone.0039156] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/18/2012] [Indexed: 11/18/2022] Open
Abstract
Mammalian DNA polymerase δ (Pol δ), a four-subunit enzyme, plays a crucial and versatile role in DNA replication and DNA repair processes. We have reconstituted human Pol δ complexes in insect cells infected with a single baculovirus into which one or more subunits were assembled. This system allowed for the efficient expression of the tetrameric Pol δ holoenzyme, the p125/p50 core dimer, the core+p68 trimer and the core+p12 trimer, as well as the p125 catalytic subunit. These were isolated in milligram amounts with reproducible purity and specific activities by a highly standardized protocol. We have systematically compared their activities in order to gain insights into the roles of the p12 and p68 subunits, as well as their responses to PCNA. The relative specific activities (apparent k(cat)) of the Pol δ holoenzyme, core+p68, core+p12 and p125/p50 core were 100, 109, 40, and 29. The corresponding apparent K(d)'s for PCNA were 7.1, 8.7, 9.3 and 73 nM. Our results support the hypothesis that Pol δ interacts with PCNA through multiple interactions, and that there may be a redundancy in binding interactions that may permit Pol δ to adopt flexible configurations with PCNA. The abilities of the Pol δ complexes to fully extend singly primed M13 DNA were examined. All the subassemblies except the core+p68 were defective in their abilities to completely extend the primer, showing that the p68 subunit has an important function in synthesis of long stretches of DNA in this assay. The core+p68 trimer could be reconstituted by addition of p12.
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Affiliation(s)
- Yajing Zhou
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Xiao Meng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
| | - Ernest Y. C. Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
| | - Marietta Y. W. T. Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
- * E-mail:
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